BN0339 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 1.4119e-06 6.6395e-04
Layer 2 2.1615e-05 6.2781e-03
Layer 5 1.4048e-04 2.1181e-02
Layer 4 9.1700e-03 6.5989e-02
Layer 6 2.7877e-02 4.4273e-02
Layer 1 9.7408e-01 6.2646e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 2.6162 0.6743
CABP1 Layer 3 2.1445 0.6105
NSF Layer 3 2.0488 0.6068
RCAN2 Layer 3 2.1250 0.5982
PRKAR1A Layer 3 2.0352 0.5881
TMOD2 Layer 3 2.1250 0.5855
LMO4 Layer 3 2.1289 0.5834
GNG3 Layer 3 2.1289 0.5833
AUXG01000058.1 Layer 3 2.1191 0.5830
INA Layer 3 2.1240 0.5828
DYNLL2 Layer 3 2.0117 0.5825
GABRA1 Layer 3 2.1582 0.5789
APP Layer 3 2.0312 0.5775
INPP5F Layer 3 2.0283 0.5768
MYO5A Layer 3 2.1582 0.5766
LYNX1 Layer 3 2.1914 0.5761
YPEL3 Layer 3 2.0586 0.5742
GAP43 Layer 3 2.1152 0.5730
RHEB Layer 3 2.0625 0.5725
SH3GL2 Layer 6 2.2051 0.5718
ATP1A1 Layer 5 2.1172 0.5679
NAT8L Layer 3 2.0215 0.5677
TUBA4A Layer 3 2.1387 0.5670
PI4KA Layer 5 1.9990 0.5664
AGAP3 Layer 3 2.0820 0.5662
NEFM Layer 3 2.4121 0.5657
UQCRH Layer 3 1.9805 0.5635
SCN8A Layer 3 2.0859 0.5627
MEF2C Layer 3 2.0684 0.5624
RGS4 Layer 2 2.1152 0.5615
PREPL Layer 6 2.0176 0.5612
MTCH1 Layer 6 1.9678 0.5602
KCNAB2 Layer 3 2.0957 0.5598
YWHAH Layer 3 1.9277 0.5594
RNPS1 Layer 3 1.9854 0.5591
RUNDC3A Layer 3 2.1016 0.5577
CRYM Layer 3 2.1514 0.5575
ACO2 Layer 3 2.1445 0.5569
FXYD7 Layer 3 2.1250 0.5566
SULT4A1 Layer 3 2.1348 0.5565
ATP6V1E1 Layer 3 1.9580 0.5561
MLLT11 Layer 3 1.9990 0.5556
ATP2B2 Layer 3 2.0547 0.5556
DNM1 Layer 3 1.9805 0.5553
RNF187 Layer 3 2.0859 0.5551
NPTN Layer 2 2.0918 0.5546
CAMK2G Layer 3 2.0938 0.5538
TPI1 Layer 3 1.9492 0.5534
SLC22A17 Layer 3 1.9678 0.5521
RAB3A Layer 3 2.0859 0.5514

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0339
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0339_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0339/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0339/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0339/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0339/report/PD/BN0339_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0339/report/PD/BN0339_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-10 23:40:49
  • Number of Processes: 10
  • Spending Time: 0h 4m